Immune response gene coexpression network analysis of Arachis hypogaea infected with Aspergillus flavus

A dual transcriptome analysis reveals accession-specific resistance responses in Lathyrus sativus against Erysiphe pisi

Lathyrus sativus (grass pea) is a valuable crop for sustainable agriculture, offering dietary benefits and desirable agronomic traits. However, its yield stability is limited by diseases such as powdery mildew caused by Erysiphe pisi. Increasing fungal resistance to pesticides and environmental concerns demand the development of resistant crop varieties. To identify key defense mechanisms and effector genes involved in the Lathyrus sativus-Erysiphe pisi interaction we analyzed four L. sativus accessions exhibiting varying resistance to E. pisi (resistant, partially resistant, partially susceptible, and susceptible) using a dual RNA-Seq experiment across different time points. We observed a host biphasic response, characterized by an initial burst of gene expression, followed by a quiescent phase, and a subsequent wave of intense gene expression. Common L. sativus defense mechanisms included antifungal protein expression, cell wall reinforcement, and reactive oxygen species-mediated defense. These defenses involved respectively Bowman-Birk type proteinase inhibitors, peptidyl-prolyl cis-trans isomerases and mannitol dehydrogenases. The resistant accession specifically activated early reinforcement of structural barriers associated with lignin biosynthesis and the phenylpropanoid pathway, along with sustained chemical defenses (e.g. eugenol synthase 1), epigenetic regulation, and oxidative stress responses thorough peroxidases and heat shock proteins. The partial resistant accession exhibited a front-loaded defense response at early infection stages. Contrastingly, the partially susceptible accession exhibited a weaker baseline defense, with a slower and less robust response targeting pathogen infection. We identified potential E. pisi effectors, including genes involved in cell wall hydrolysis (e.g. mannosidase DCW1), nutrient acquisition (e.g. secreted alpha-glucosidase), and virulence (e.g. SnodProt1), with a higher diversity of effectors identified in the susceptible accession. In conclusion, this study identifies novel targets such as NLRs and effectors, antifungal proteins and genes related to cell wall reinforcement, within the complex Lathyrus sativus-Erysiphe pisi interaction to support future breeding programs aimed at enhancing resistance to E. pisi in L. sativus and related species.

Identification and Characterization of Peanut Seed Coat Secondary Metabolites Inhibiting Aspergillus flavus Growth and Reducing Aflatoxin Contamination

The peanut seed coat acts as a physical and biochemical barrier against Aspergillus flavus infection; however, the nature of the inhibitory chemicals in the peanut seed coat in general is not known. This study identified and characterized peanut seed coat metabolites that inhibit A. flavus growth and aflatoxin contamination. Selected peanut accessions grown under well-watered and water-deficit conditions were assayed for A. flavus resistance, and seed coats were metabolically profiled using liquid chromatography mass spectrometry. Kyoto Encyclopedia of Genes and Genome phenylpropanoid pathway reference analysis resulted in the identification of several seed coat metabolic compounds, and ten selected metabolites were tested for inhibition of A. flavus growth and aflatoxin contamination. Radial growth bioassay demonstrated that 2,5-dihydroxybenzaldehyde inhibited A. flavus growth (98.7%) and reduced the aflatoxin contamination estimate from 994 to 1 μg/kg. Scanning electron micrographs showed distorted hyphae and conidiophores in cultures of 2,5-dihydroxybenzaldehyde-treated A. flavus, indicating its potential use for field application as well as seed coat metabolic engineering.

The Autophagy-Related Protein ATG8 Orchestrates Asexual Development and AFB1 Biosynthesis in Aspergillus flavus

Autophagy, a conserved cellular recycling process, plays a crucial role in maintaining homeostasis under stress conditions. It also regulates the development and virulence of numerous filamentous fungi. In this study, we investigated the specific function of ATG8, a reliable autophagic marker, in the opportunistic pathogen Aspergillus flavus. To investigate the role of atg8 in A. flavus, the deletion and complemented mutants of atg8 were generated according to the homologous recombination principle. Deletion of atg8 showed a significant decrease in conidiation, spore germination, and sclerotia formation compared to the WT and atg8C strains. Additionally, aflatoxin production was found severely impaired in the ∆atg8 mutant. The stress assays demonstrated that ATG8 was important for A. flavus response to oxidative stress. The fluorescence microscopy showed increased levels of reactive oxygen species in the ∆atg8 mutant cells, and the transcriptional result also indicated that genes related to the antioxidant system were significantly reduced in the ∆atg8 mutant. We further found that ATG8 participated in regulating the pathogenicity of A. flavus on crop seeds. These results revealed the biological role of ATG8 in A. flavus, which might provide a potential target for the control of A. flavus and AFB1 biosynthesis.

Thaumatin-like Proteins in Legumes: Functions and Potential Applications-A Review

Thaumatin-like proteins (TLPs) comprise a complex and evolutionarily conserved protein family that participates in host defense and several developmental processes in plants, fungi, and animals. Importantly, TLPs are plant host defense proteins that belong to pathogenesis-related family 5 (PR-5), and growing evidence has demonstrated that they are involved in resistance to a variety of fungal diseases in many crop plants, particularly legumes. Nonetheless, the roles and underlying mechanisms of the TLP family in legumes remain unclear. The present review summarizes recent advances related to the classification, structure, and host resistance of legume TLPs to biotic and abiotic stresses; analyzes and predicts possible protein-protein interactions; and presents their roles in phytohormone response, root nodule formation, and symbiosis. The characteristics of TLPs provide them with broad prospects for plant breeding and other uses. Searching for legume TLP genetic resources and functional genes, and further research on their precise function mechanisms are necessary.

Transcriptomic and Metabolomic Analyses of the Response of Resistant Peanut Seeds to Aspergillus flavus Infection

Peanut seeds are susceptible to Aspergillus flavus infection, which has a severe impact on the peanut industry and human health. However, the molecular mechanism underlying this defense remains poorly understood. The aim of this study was to analyze the changes in differentially expressed genes (DEGs) and differential metabolites during A. flavus infection between Zhonghua 6 and Yuanza 9102 by transcriptomic and metabolomic analysis. A total of 5768 DEGs were detected in the transcriptomic study. Further functional analysis showed that some DEGs were significantly enriched in pectinase catabolism, hydrogen peroxide decomposition and cell wall tissues of resistant varieties at the early stage of infection, while these genes were differentially enriched in the middle and late stages of infection in the nonresponsive variety Yuanza 9102. Some DEGs, such as those encoding transcription factors, disease course-related proteins, peroxidase (POD), chitinase and phenylalanine ammonialyase (PAL), were highly expressed in the infection stage. Metabolomic analysis yielded 349 differential metabolites. Resveratrol, cinnamic acid, coumaric acid, ferulic acid in phenylalanine metabolism and 13S-HPODE in the linolenic acid metabolism pathway play major and active roles in peanut resistance to A. flavus. Combined analysis of the differential metabolites and DEGs showed that they were mainly enriched in phenylpropane metabolism and the linolenic acid metabolism pathway. Transcriptomic and metabolomic analyses further confirmed that peanuts infected with A. flavus activates various defense mechanisms, and the response to A. flavus is more rapid in resistant materials. These results can be used to further elucidate the molecular mechanism of peanut resistance to A. flavus infection and provide directions for early detection of infection and for breeding peanut varieties resistant to aflatoxin contamination.

Advances in omics research on peanut response to biotic stresses

Peanut growth, development, and eventual production are constrained by biotic and abiotic stresses resulting in serious economic losses. To understand the response and tolerance mechanism of peanut to biotic and abiotic stresses, high-throughput Omics approaches have been applied in peanut research. Integrated Omics approaches are essential for elucidating the temporal and spatial changes that occur in peanut facing different stresses. The integration of functional genomics with other Omics highlights the relationships between peanut genomes and phenotypes under specific stress conditions. In this review, we focus on research on peanut biotic stresses. Here we review the primary types of biotic stresses that threaten sustainable peanut production, the multi-Omics technologies for peanut research and breeding, and the recent advances in various peanut Omics under biotic stresses, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics and phenomics, for identification of biotic stress-related genes, proteins, metabolites and their networks as well as the development of potential traits. We also discuss the challenges, opportunities, and future directions for peanut Omics under biotic stresses, aiming sustainable food production. The Omics knowledge is instrumental for improving peanut tolerance to cope with various biotic stresses and for meeting the food demands of the exponentially growing global population.

Transcriptome analysis reveals the mechanisms of hepatic injury caused by long-term environmental exposure to atrazine in juvenile common carp (Cyprinus carpio L.)

Atrazine (ATZ) is the second most commonly used herbicide worldwide, resulting in the pollution of water bodies and affecting the economic benefits of aquaculture. ATZ is known to cause liver damage in the common carp, Cyprinus carpio L., one of the most widely cultivated fish in China, but the underlying mechanisms are poorly understood. In this study, juvenile common carp Cyprinus carpio L. were exposed to three different environmental levels (0.4, 0.8, and 1.2 μg/L) of ATZ for 12 weeks and changes in the liver transcriptomes between the high-dose group and the control group were analyzed. The data showed that different levels of ATZ exposure caused hepatotoxicity in juvenile carp, shown by biochemical parameters and histopathological changes. Comparative transcriptomics showed that high-dose ATZ exposure led to alterations in the expression of various lipid metabolism-related gene changes, including genes associated with metabolic pathways, fatty acid metabolism, and fatty acid elongation. Furthermore, a connection network analysis of the top 100 differentially expressed genes (DEGs) showed a variety of associations between high-dose ATZ-induced liver damage and the principal DEGs, indicating the complexity of hepatotoxicity induced by ATZ. In conclusion, the molecular mechanisms underlying ATZ-triggered hepatotoxicity in juvenile carp are primarily related to impaired lipid metabolism.

Comparative transcriptome profiling and weighted gene co-expression network analysis to identify core genes in maize (Zea mays L.) silks infected by multiple fungi

Maize (Zea mays L.) is the third most popular Poaceae crop after wheat and rice and used in feed and pharmaceutical sectors. The maize silk contains bioactive components explored by traditional Chinese herbal medicine for various pharmacological activities. However, Fusarium graminearum, Fusarium verticillioides, Trichoderma atroviride, and Ustilago maydis can infect the maize, produce mycotoxins, hamper the quantity and quality of silk production, and further harm the primary consumer's health. However, the defense mechanism is not fully understood in multiple fungal infections in the silk of Z. mays. In this study, we applied bioinformatics approaches to use the publicly available transcriptome data of Z. mays silk affected by multiple fungal flora to identify core genes involved in combatting disease response. Differentially expressed genes (DEGs) were identified among intra- and inter-transcriptome data sets of control versus infected Z. mays silks. Upon further comparison between up- and downregulated genes within the control of datasets, 4,519 upregulated and 5,125 downregulated genes were found. The DEGs have been compared with genes in the modules of weighted gene co-expression network analysis to relevant specific traits towards identifying core genes. The expression pattern of transcription factors, carbohydrate-active enzymes (CAZyme), and resistance genes was analyzed. The present investigation is supportive of our findings that the gene ontology, immunity stimulus, and resistance genes are upregulated, but physical and metabolic processes such as cell wall organizations and pectin synthesis were downregulated respectively. Our results are indicative that terpene synthase TPS6 and TPS11 are involved in the defense mechanism against fungal infections in maize silk.

Transcriptomic and proteomic analysis of Chinese rare minnow (Gobiocypris rarus) larvae in response to acute waterborne cadmium or mercury stress

In this study, Chinese rare minnow (Gobiocypris rarus) larvae were exposed to the control group, Cd concentrations (0.5 and 2.5 mg/L), and Hg concentrations (0.1 and 0.3 mg/L) for 96 h. Transcriptome analysis showed that 816 and 1599 significantly differentially expressed genes (DEGs) were identified in response to 2.5 mg/L Cd²⁺ and 0.3 mg/L Hg²⁺, respectively. Functional enrichment analysis revealed that DEGs were mostly associated with immune responses after Cd exposure, such as antigen processing and presentation, phagosome, apoptosis, and lysosome. Similarly, functional enrichment analysis showed that many pathways were mostly involved in metabolism after Hg exposure, such as glutathione metabolism and starch and sucrose metabolism. Results of two-dimensional electrophoresis (2-DE) showed that the abundance of 10 protein spots was significantly altered in the Cd²⁺ treatments. The proteomic analysis demonstrated that Cd toxicity might impair cytoskeletal and cell motility-related protein activity in the liver of G. rarus. Similarly, the abundance of 24 protein spots was significantly altered in the Hg²⁺ treatments. Hg toxicity regulates the expression of proteins belonging to several functional categories, including cytoskeleton, oxidative stress, digestive system, and energy metabolism. This study provides valuable relevant insight into the molecular mechanisms in response to Cd or Hg toxicity in aquatic organisms and will help screen for potential biomarkers to respond to Cd and Hg pollutants.